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If you didn't know, Navi was never found when she vanished at the end of OoT. So, Link set out to find her (WHY?) when Skull Kid messed with him, causing Majora's Mask. But whatever happened to Navi, even though nobody ever cared? Well, I can tell you in a few words.

Once the Master Sword was back in it's resting place, Link stood there like an idiot for about 20 seconds, doing nothing interesting at all. Then, Navi said this very powerful statement:

bye pleb

Then Navi flew off, majestically out the window...

That's not true.

Link was observant, and he said "OH CRAP! NAVI WATCH OUT THE WINDOWS ISN'T OPEN!!!"
But it was too late. Navi flew out and....

*splat*

And that's it. This is why Majora's Mask existed in the first place. But who cares? It's a good game.